Questions about sequin used about sg-nex-data HOT 2 OPEN

Would like to know as well. I found the reformatted gtf contains bambu generated transcripts with sequin, but not sure if these are complete sequin transcripts.

from sg-nex-data.

Hi,

Sorry for getting back lately.

For the sequin reference, you may download the fasta and gtf file using the links below:

gtf file: http://sg-nex-data.s3.amazonaws.com/data/annotations/gtf_file/hg38_sequins_SIRV_ERCCs_longSIRVs_v5_reformatted.gtf
this is the complete gtf file that we used for our analysis, for your case, you can subset the gtf file to only sequin annotations, filtering by either sequin gene or transcript names
fasta file:
http://sg-nex-data.s3.amazonaws.com/data/annotations/genome_fasta/hg38_sequins_SIRV_ERCCs_longSIRVs.fa
similarly for the fasta file, you can also extract only the sequences for sequins by looking at chrIS only

For the sequin concentration, we have recently added the concentration file that we have used for the original manuscript: https://github.com/GoekeLab/sg-nex-data/blob/master/docs/RNAsequins_MixA.xlsx

Let me know you still have issues related to this.

Thank you

from sg-nex-data.